Abstract
Huanglongbing (HLB), or citrus greening, is the most devastating disease in citrus worldwide. Commercial citrus varieties including sweet orange (Citrus sinensis) are highly susceptible to HLB, and trifoliate orange (Poncirus trifoliata, a close Citrus relative) is widely considered resistant or highly tolerant to HLB. In this study, an intergeneric F1 population of sweet orange and trifoliate orange was genotyped by Genotyping-by-Sequencing, and high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange. The two genetic maps exhibited high synteny and high coverage of the citrus genome. Progenies of the F1 population and their parents were planted in a replicated field trial, exposed to intense HLB pressure for 3 years, and then evaluated for susceptibility to HLB over 2 years. The F1 population exhibited a wide range in severity of HLB foliar symptom and canopy damage. Genome-wide QTL analysis based on the phenotypic data of foliar symptom and canopy damage in 2 years identified three clusters of repeatable QTLs in trifoliate orange linkage groups LG-t6, LG-t8 and LG-t9. Co-localization of QTLs for two traits was observed within all three regions. Additionally, one cluster of QTLs in sweet orange (linkage group LG-s7) was also detected. The majority of the identified QTLs each explained 18–30% of the phenotypic variation, indicating their major role in determining HLB responses. These results show, for the first time, a quantitative genetic nature yet the presence of major loci for the HLB tolerance in trifoliate orange. The results suggest that sweet orange also contains useful genetic factor(s) for improving HLB tolerance in commercial citrus varieties. Findings from this study should be very valuable and timely to researchers worldwide as they are hastily searching for genetic solutions to the devastating HLB crisis through breeding, genetic engineering, or genome editing.
Highlights
Huanglongbing (HLB), commonly known as citrus greening, is the most devastating disease in citrus plantations worldwide
HLB is generally considered to be caused by three species of Candidatus Liberibacter, of which Candidatus Liberibacter asiaticus (CLas) is the most widespread and virulent species and is the only species reported in the citrus industry of United States
After alignment with the reference genome, the average number of read clusters was 1.83E5 and 1.47E5 for trifoliate oranges and sweet oranges, respectively, and the numbers of read clusters for the F1 progenies ranged from 0.32E5 to 2.79E5 and averaged to be 1.03E5
Summary
Huanglongbing (HLB), commonly known as citrus greening, is the most devastating disease in citrus plantations worldwide. Since the first identification of the disease in Florida in 2005, HLB has spread throughout the state, and is found in most states in the United States where citrus is grown. It is rapidly spreading throughout many of the world’s production areas, as well. Huanglongbing-diseased trees develop leaves with characteristic blotchy mottle, the shoots are stunted and yellowing, and the canopy and branches gradually dieback as the disease progresses These symptoms are associated with the host limitations for photoassimilate transport and nutrient uptake induced by the disease, and can lead to tree death (Blaustein et al, 2018). High levels of tolerance to HLB were mostly found in some types that are commonly used as rootstocks, such as trifoliate orange and some of its hybrids (Albrecht and Bowman, 2011, 2012; Ramadugu et al, 2016)
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